Another lesson learnt.
After having to remove the new 4.6 engine again (another V8 engine failure) I noticed that the first motion shaft from the gear-box was not fully engaging the clutch center plate, in fact there was less that 10mm of engagement in the splines and the splines in the center plate are starting to distort. In hindsight this is evident in the photos taken through the hole in the bell-housing when the prop failed (Bottom pic).
Some research ensued and what I have learnt I shall repeat here for anyone that reads these pages.
The pictures above show two flywheels and clutch assemblies, and below the centre plates.
The flywheel on the left is an SD1 flywheel with the 7.5" clutch assembly (the clutch fitted to the Defender 200 & 300 TDI's)
Many people reportedly like the SD1 flywheel as it is lighter and using the smaller clutch assembly also means a reduced mass on the rear of the engine (better acceleration).
The flywheel on the right is a discovery 4.0 litre with the 10.5" clutch assembly as fitted to the majority of later Land Rover products with the V8 engines. As you will see it has a larger mass.
So in my case I am using a R380 gearbox from a Discovery and it would appear that the bell-housing is slightly longer/deeper than the LT77 gearbox bell-housing etc. used in the SD1 car. The result is that the first-motion shaft will not engage the clutch center plate properly.
The difference is that the Land Rover flywheel is substantially thicker, this locates the alignment of the clutch center plate toward the gearbox improving the centre plate engagement on the first-motion shaft by as much as 10mm.
The clutch center plate boss is also "higher" so again improving engagement.
The larger clutch cover also stands taller this may help explain why I was having difficulty getting the clutch to operate smoothly using the earlier SD1 flywheel and clutch assembly.
At time of writing this I have not driven the new assembly so cannot report if there are any improvements or drawbacks using the “correct” flywheel.